Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate AO356_30225 AO356_30225 choline dehydrogenase
Query= metacyc::MONOMER-15202 (579 letters) >lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_30225 AO356_30225 choline dehydrogenase Length = 546 Score = 356 bits (914), Expect = e-102 Identities = 216/546 (39%), Positives = 312/546 (57%), Gaps = 27/546 (4%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95 +DYIVVGAG++GC +A LS DP N VLLIEAG + W++ P G N +W F Sbjct: 4 YDYIVVGAGSSGCPVARGLSDDPRNNVLLIEAGPASDRFWVNTPAGMGKLYFNKSLNWNF 63 Query: 96 RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155 RT P L GR + +PRGK LGG SSINGM+++RG +D+DGW L G+ W +++ LP Sbjct: 64 RTSPMEKLQGRRMYWPRGKLLGGSSSINGMVFIRGHQKDFDGWRAL-GNPGWGYEDVLPY 122 Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRDF 215 F + E + GGD ++ G G I +K + DF AA G+P T D Sbjct: 123 FKKME---HFERGGD------EYRGANGPLWISDPVVKEKSSYDFIEAANRIGIPVTEDM 173 Query: 216 NRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPRC 275 N ++GV + N + G R + +AF+ V +R NLTV ++ ++ F EG Sbjct: 174 NGALHDGVGFMQHNIQDGQRMSTYRAFIEPVIERPNLTVRTGCELQRVLF---EGR--TA 228 Query: 276 CGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVGE 335 G+ V ++G+ A EV+LSAG++ +PQ+L LSGIGP A L +HAIP V + PGVG+ Sbjct: 229 VGIEVLKSGRLERIYAAREVILSAGSLKTPQMLMLSGIGPRAELEKHAIPEVLNSPGVGQ 288 Query: 336 NLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKI--GLEYILKRSGPMSMAPSQLCIFTRS 393 NLQDH I + ++ + N +L+G K G Y++ R G +++ SQ+ F +S Sbjct: 289 NLQDHFYIHTAFRCTPDSSYNA---NLVGLRKYWEGFRYLMTRKGYLALGSSQVAAFVKS 345 Query: 394 SKEYEHPNLEYHVQPLSLEAFGQPLHD---FPAITASVCNLNPTSRGTVRIKSGNPRQAP 450 S + ++ +L+ +P++ + F D P + SV L P++ GTV ++S NP Sbjct: 346 SPDEDYADLQISFRPMTFQYFPDGTVDVERHPGLGVSVYQLRPSTTGTVTLRSTNPSDPA 405 Query: 451 AISPNYLSTEEDRQVAADSLRVTRHIA-SQPAFAKYDPEEFKPGVQYQSDEDLARLAGDI 509 +PN+LS++ D +R R I S+P ++ EE PG+ ++DED+ + Sbjct: 406 DYTPNFLSSDYDVNAVISGVRWIRKIMNSEPIKSRVVSEEL-PGLHIRTDEDIYNYLVET 464 Query: 510 GTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAE 569 G + H GT KMG +D MAVVD LRVRG+ LRVVDASIMP ITSGNTN+P++MI Sbjct: 465 GNSAHHQGGTCKMG--NDAMAVVDERLRVRGIERLRVVDASIMPFITSGNTNAPSIMIGV 522 Query: 570 KAAGWI 575 KAA I Sbjct: 523 KAADLI 528 Lambda K H 0.318 0.135 0.418 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 882 Number of extensions: 39 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 579 Length of database: 546 Length adjustment: 36 Effective length of query: 543 Effective length of database: 510 Effective search space: 276930 Effective search space used: 276930 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory